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- PDB-6rzr: Structure of IMP-13 metallo-beta-lactamase complexed with hydroly... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rzr | ||||||||||||
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Title | Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed imipenem | ||||||||||||
![]() | Beta-lactamase | ||||||||||||
![]() | HYDROLASE / metallo-beta-lactamase | ||||||||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Zak, K.M. / Softley, C. / Kolonko, M. / Sattler, M. / Popowicz, G.M. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase. Authors: Softley, C.A. / Zak, K.M. / Bostock, M.J. / Fino, R. / Zhou, R.X. / Kolonko, M. / Mejdi-Nitiu, R. / Meyer, H. / Sattler, M. / Popowicz, G.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r73C ![]() 6r78C ![]() 6r79SC ![]() 6rzsC ![]() 6s0hC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25167.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.5 Å / Num. obs: 42307 / % possible obs: 99.24 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.99 / Net I/av σ(I): 11.65 / Net I/σ(I): 11.65 |
Reflection shell | Resolution: 1.9→1.96 Å / Num. unique obs: 4082 / CC1/2: 0.75 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6R79 Resolution: 1.9→45.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.49 Å2 / Biso mean: 45.296 Å2 / Biso min: 25.2 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.951 Å / Total num. of bins used: 20
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